ArticleNature biotechnology2024
Pangenome graph construction from genome alignments with Minigraph-Cactus.
Article in Nature biotechnology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 217 papers.
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Who cites it
217 citing papers in PubMed.
- An Icelandic pangenome reference.Nature · 2026Article
- Article
- Pan-genomics and multi-omics for deciphering genetic variation and accelerating genetic improvement in ruminant livestock.Functional & integrative genomics · 2026Review
- Defining and cataloging variants in pangenome graphs.Cell genomics · 2026Article
- Pangenomic analyses in the cultivated grapevine confirm high genomic collinearity and extensive dispensable gene content likely involved in adaptation.G3 (Bethesda, Md.) · 2026Article
- Long-read low-pass sequencing enhances variant detection in a peanut MAGIC population.G3 (Bethesda, Md.) · 2026Article
- ONT-only genome assembly of a Korean male individual using a semen sample.Genes & genomics · 2026Article
- A pangenome framework uncovers the role of deletions in repeated evolution of cave-derived traits.Genome research · 2026Article
- Four haplotype-resolved genome assemblies and a reference-free 66-haplotype pangenome graph for Cannabis sativa.Scientific data · 2026Article
- Telomere-to-telomere genome assembly and a pangenome for the rat.Cell genomics · 2026Article
- On the ancestry and evolution of the extinct dire wolf.Cell genomics · 2026Article
- A complete genome for the common marmoset.Cell · 2026Article
- gaftools: a toolkit for analyzing and manipulating pangenome alignments.Bioinformatics (Oxford, England) · 2026Article
- PangyPlot: multi-scale interactive visualization of pangenome variation graphs.Bioinformatics (Oxford, England) · 2026Article
- Rare disease genomics in an era of human pangenomics and telomere-to-telomere genome references.European journal of human genetics : EJHG · 2026Review
- HPRC2: A human pangenome reference with near-complete coverage of common genetic variation.bioRxiv : the preprint server for biology · 2026Article
- [Applications and Challenges of Deep Learning in Human Genome Research].Sichuan da xue xue bao. Yi xue ban = Journal of Sichuan University. Medical science edition · 2026Review
- NodeGWAS: Leveraging graph pangenomes for sensitive and accurate association analyses across diverse diploid and polyploid species.Plant communications · 2026Article
- GBZ-base and GAF-base: Indexed pangenome file formats.bioRxiv : the preprint server for biology · 2026Article
- De Bruijn graphs for pangenomics: in-depth performance benchmarking of de Bruijn graph-based tools for read mapping.Briefings in bioinformatics · 2026Article
157 more citing papers are in PubMed but not listed here.
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Authors and funding
10 authors.
Funding
Abstract
Pangenome references address biases of reference genomes by storing a representative set of diverse haplotypes and their alignment, usually as a graph. Alternate alleles determined by variant callers can be used to construct pangenome graphs, but advances in long-read sequencing are leading to widely available, high-quality phased assemblies. Constructing a pangenome graph directly from assemblies, as opposed to variant calls, leverages the graph's ability to represent variation at different scales. Here we present the Minigraph-Cactus pangenome pipeline, which creates pangenomes directly from whole-genome alignments, and demonstrate its ability to scale to 90 human haplotypes from the Human Pangenome Reference Consortium. The method builds graphs containing all forms of genetic variation while allowing use of current mapping and genotyping tools. We measure the effect of the quality and completeness of reference genomes used for analysis within the pangenomes and show that using the CHM13 reference from the Telomere-to-Telomere Consortium improves the accuracy of our methods. We also demonstrate construction of a Drosophila melanogaster pangenome.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.